Related papers: Knot-detection algorithm to measure viscosity in t…

Proteins are linear molecular chains that often fold to function. The topology of folding is widely believed to define its properties and function, and knot theory has been applied to study protein structure and its implications. More that…

Knots are entangled structures that cannot be untangled without a cut. Topological stability of knots is one of the many examples of their important properties that can be used in information storage and transfer. Knot dynamics is important…

This paper is an introduction to the subject of virtual knot theory, combined with a discussion of some specific new theorems about virtual knots. The new results are as follows: We prove, using a 3-dimensional topology approach that if a…

Let $M$ be a connected, closed, oriented three-manifold and $K$, $L$ two rationally null-homologous oriented simple closed curves in $M$. We give an explicit algorithm for computing the linking number between $K$ and $L$ in terms of a…

The ropelength of a knot is the minimum contour length of a tube of unit radius that traces out the knot in three dimensional space without self-overlap, colloquially the minimum amount of rope needed to tie a given knot. Theoretical upper…

We use technology from sutured manifold theory and the theory of Heegaard splittings to relate genus reducing crossing changes on knots in S^3 to twists on surfaces arising in circular Heegaard splittings for knot complements. In a separate…

We make use of the 3D nature of knots and links to find savings in computational complexity when computing knot invariants such as the linking number and, in general, most finite type invariants. These savings are achieved in comparison…

The most tight conformations of prime knots are found with the use of the SONO algorithm. Their curvature and torsion profiles are calculated. Symmetry of the knots is analysed. Connections with the physics of polymers are discussed.

The altenating knots, links and twists projected on the S_2 sphere are identified with the phase Space of a Hamiltonian dynamic system of one degree of freedom. The saddles of the system correspond to the crossing points, the edges, to the…

We present a new method for the statistical process control of lattice structures using tools from Topological Data Analysis. Motivated by applications in additive manufacturing, such as aerospace components and biomedical implants, where…

Recent studies classify the topology of proteins by analysing the distribution of their projections using knotoids. The approximation of this distribution depends on the number of projection directions that are sampled. Here we investigate…

We introduce a notion of intrinsic linking and knotting for virtual spatial graphs. Our theory gives two filtrations of the set of all graphs, allowing us to measure, in a sense, how intrinsically linked or knotted a graph is; we show that…

We present a systematic classification of uncolored bonded knots with singularity number at most seven. Bonded knots provide a topological model for closed protein chains with intramolecular bridges, such as disulfide bonds. Following the…

Knotted and tangled structures frequently appear in physical fields, but so do mechanisms for untying them. To understand how this untying works, we simulate the behavior of 1,458 superfluid vortex knots of varying complexity and scale in…

We extend the entanglement bootstrap approach to (3+1)-dimensions. We study knotted excitations of (3+1)-dimensional liquid topological orders and exotic fusion processes of loops. As in previous work in (2+1)-dimensions, we define a…

Entanglement and its propagation are central to understanding a multitude of physical properties of quantum systems. Notably, within closed quantum many-body systems, entanglement is believed to yield emergent thermodynamic behavior.…

We study RNA foldings and investigate their topology using a combination of knot theory and embedded rigid vertex graphs. Knot theory has been helpful in modeling biomolecules, but classical knots place emphasis on a biomolecule's…

Using a structure-based coarse-grained model of proteins, we study the mechanism of unfolding of knotted proteins through heating. We find that the dominant mechanisms of unfolding depend on the temperature applied and are generally…

Meier and Zupan showed that every surface in the four-sphere admits a bridge trisection and can therefore be represented by three simple tangles. This raises the possibility of applying methods from link homology to knotted surfaces. We use…

We develop topological methods for analyzing difference topology experiments involving 3-string tangles. Difference topology is a novel technique used to unveil the structure of stable protein-DNA complexes involving two or more DNA…